Hi Alec,
Thank you for your answer.
I am afraid I cannot fully understand your comments. Here's the definition
of the fold 80 base penalty from Picard:
FOLD_80_BASE_PENALTY: The fold over-coverage necessary to raise 80% of
bases in "non-zero-cvg" targets to the mean coverage level in those targets.
According to the definition it is not required that more than 80% of the
bases in the target should have coverage.
What I understand is that the fold 80 base penalty is the fold
over-coverage needed to raise 80% of bases in covered targets to the mean
coverage. As far as I see it, it should not matter how many bases are
actually covered in the target.
What do you think?
Thank you all once again.
Best wishes,
Esteban
El martes, 27 de mayo de 2014, Alec Wysoker
<al...@broadinstitute.org<javascript:_e(%7B%7D,'cvml','al...@broadinstitute.org');>>
escribió:
> Hi Esteban,
>
> Less than 80% of the bases in targets that have non-zero coverage have any
> coverage at all. The program can't know how many times more sequencing
> would be required to raise 80% of bases to mean coverage, so it returns
> infinity.
>
> -Alec
>
> On May 27, 2014, at 5:54 AM, Esteban Czwan <ecz...@gmail.com> wrote:
>
> > Dear all,
> >
> > I calculated Picard HsMetrics and the FOLD_80_BASE_PENALTY metric had
> > a question mark ("?").
> >
> > I have attached the output file to this email.
> >
> > Do you know what might have happened?
> >
> > Thank you and best wishes,
> >
> > Esteban
> >
> <EXOMEV3_KAPA_1_microgram_subsample_calculate_hs_metrics.txt>------------------------------------------------------------------------------
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